
4 GPU(s) detected.

Patched coupled.in -> num_procs = 4 (SLURM_GPUS_ON_NODE='4')
/home/users/sajagbe2/.local/lib/python3.11/site-packages/pyscf/dft/libxc.py:511: UserWarning: Since PySCF-2.3, B3LYP (and B3P86) are changed to the VWN-RPA variant, corresponding to the original definition by Stephens et al. (issue 1480) and the same as the B3LYP functional in Gaussian. To restore the VWN5 definition, you can put the setting "B3LYP_WITH_VWN5 = True" in pyscf_conf.py
  warnings.warn('Since PySCF-2.3, B3LYP (and B3P86) are changed to the VWN-RPA variant, '


============================================================
                   Electrostatic Map Suite
                    By Stephen O. Ajagbe
============================================================

============================================================
              Electrostatic Potential Module
============================================================

Generating VDW surface for potential mapping...
Generating VDW surface (density=0.5, scale=1.0)...
Generated 157 surface points
Surface saved to: _potential_tmp.surf (157 points)
Computed Gauss-law surface charges from APBS potential and dielectric maps
Surface saved to: coupled_triplet.surf (157 points)
Potential map CSV: coupled_triplet.csv
============================================================
============================================================
                  Electrostatic Tuning Maps
             Built on efforts by the Gozem Lab
   See: https://pubs.acs.org/doi/10.1021/acs.jpcb.9b00489
============================================================



4 GPU(s) detected.

Calculating Tuning of:  ['exe']
Using molecular states: {'neutral': True, 'td': True}


============================================================
                Calculation Type: combined
                Number of surface points: 157
                Parallel Processing: True
============================================================


Logging results to: logs_20260905_170738
converged SCF energy = -1896.66485107834
Spin 0 (2S+1=1) converged: E = -1896.664851 Ha

Lowest energy: spin=0 (2S+1=1), E=-1896.664851 Ha
Saving GPU object type: <class 'gpu4pyscf.dft.rks.RKS'>
Saving functional (from parameter): b3lyp
Saved to molecule_alone.chk, Energy: -1896.664851078343 (GPU)
Multi-GPU detected. Using subprocess for single-GPU TDDFT...
TDDFT completed in subprocess on GPU 0, states: 3


============================================================
                Raw Properties (No Surface)
                Total raw properties calculated: 3
                t1_exe: 0.320697
                t2_exe: 0.473287
                t3_exe: 1.300499
============================================================


Running combined calculation with all 157 surface points...
Summary log initialized: logs_20260905_170738/calculation_summary.out

=== Resurrecting /data/PHO_WORK/sajagbe2/QMMM/LOVCalculations/lf-proto/sog-protein-step0/coupled-combined/MSOG/triplet/molecule_alone.chk ===
Loaded XC functional: b3lyp
Creating DFT object with xc=b3lyp
Converting <class 'pyscf.dft.rks.RKS'> to GPU...
Successfully converted to GPU: <class 'gpu4pyscf.dft.rks.RKS'>


******** <class 'gpu4pyscf.dft.rks.RKS'> ********
method = RKS
initial guess = chkfile
damping factor = 0
level_shift factor = 0
DIIS = <class 'gpu4pyscf.scf.diis.CDIIS'>
diis_start_cycle = 1
diis_space = 8
diis_damp = 0
SCF conv_tol = 1e-09
SCF conv_tol_grad = None
SCF max_cycles = 50
direct_scf = True
direct_scf_tol = 1e-13
chkfile to save SCF result = /tmp/tmpor9s0vzq.chk
max_memory 4000 MB (current use 1710 MB)
XC library gpu4pyscf.dft.libxc version 7.0.0 (CUDA)
    unable to decode the reference due to https://github.com/NVIDIA/cuda-python/issues/29
XC functionals = b3lyp
small_rho_cutoff = 1e-07
Set gradient conv threshold to 3.16228e-05
init E= -1896.66485107829
  HOMO = 0.0555528412507914  LUMO = 0.0664049042518164
cycle= 1 E= -1896.66485095513  delta_E= 1.23e-07  |g|= 0.000519  |ddm|= 0.000961
  HOMO = 0.0556850486005745  LUMO = 0.0663799221337494
cycle= 2 E= -1896.66471333839  delta_E= 0.000138  |g|= 0.0174  |ddm|= 0.0319
  HOMO = 0.0555576662193849  LUMO = 0.0664042147047674
cycle= 3 E= -1896.66485107651  delta_E= -0.000138  |g|= 6.53e-05  |ddm|= 0.0308
  HOMO = 0.0555573180535233  LUMO = 0.0664040867775914
cycle= 4 E= -1896.66485107744  delta_E= -9.34e-10  |g|= 4.53e-05  |ddm|= 3.71e-05
  HOMO = 0.0555569990701833  LUMO = 0.0664041159044883
cycle= 5 E= -1896.66485107825  delta_E= -8.09e-10  |g|= 1.51e-05  |ddm|= 5.44e-05
converged SCF energy = -1896.66485107825
Resurrected GPU DFT object: <class 'gpu4pyscf.dft.rks.RKS'>, Energy: -1896.6648510782484
Multi-GPU detected. Using subprocess for single-GPU TDDFT...
TDDFT completed in subprocess on GPU 0, states: 3


******** <class 'gpu4pyscf.dft.rks.RKS'> ********
method = RKS
initial guess = chkfile
damping factor = 0
level_shift factor = 0
DIIS = <class 'gpu4pyscf.scf.diis.CDIIS'>
diis_start_cycle = 1
diis_space = 8
diis_damp = 0
SCF conv_tol = 1e-09
SCF conv_tol_grad = None
SCF max_cycles = 50
direct_scf = True
direct_scf_tol = 1e-13
chkfile to save SCF result = molecule_alone.chk
max_memory 4000 MB (current use 1805 MB)
XC library gpu4pyscf.dft.libxc version 7.0.0 (CUDA)
    unable to decode the reference due to https://github.com/NVIDIA/cuda-python/issues/29
XC functionals = b3lyp
small_rho_cutoff = 1e-07
Overwritten attributes  get_hcore energy_nuc  of <class 'gpu4pyscf.dft.rks.RKS'>
<class 'gpu4pyscf.dft.rks.RKS'> does not have attributes  basis charge spin
Set gradient conv threshold to 3.16228e-05
init E= -1896.71492845365
  HOMO = 0.0337492987509982  LUMO = 0.0470274737772003
cycle= 1 E= -1896.70423761576  delta_E= 0.0107  |g|= 0.149  |ddm|= 0.358
  HOMO = 0.069745413534707  LUMO = 0.0939892740695762
cycle= 2 E= -1896.0614891487  delta_E= 0.643  |g|= 1.11  |ddm|= 2.11
  HOMO = 0.0409008749394958  LUMO = 0.0486142525612799
cycle= 3 E= -1896.54618124929  delta_E= -0.485  |g|= 0.602  |ddm|= 1.27
  HOMO = 0.0377980485972446  LUMO = 0.0473276404343098
cycle= 4 E= -1896.71431156988  delta_E= -0.168  |g|= 0.052  |ddm|= 1.05
  HOMO = 0.0377096786184969  LUMO = 0.0469643431559199
cycle= 5 E= -1896.71321808278  delta_E= 0.00109  |g|= 0.0687  |ddm|= 0.191
  HOMO = 0.0373467469580378  LUMO = 0.0473939972294261
cycle= 6 E= -1896.71219502338  delta_E= 0.00102  |g|= 0.0825  |ddm|= 0.0343
  HOMO = 0.0371213974446091  LUMO = 0.0474452433460307
cycle= 7 E= -1896.71368863632  delta_E= -0.00149  |g|= 0.0588  |ddm|= 0.0419
  HOMO = 0.0369576629633117  LUMO = 0.0474586828523813
cycle= 8 E= -1896.71460035845  delta_E= -0.000912  |g|= 0.0381  |ddm|= 0.0366
  HOMO = 0.0367027331790259  LUMO = 0.0474715234307776
cycle= 9 E= -1896.71523948322  delta_E= -0.000639  |g|= 0.00791  |ddm|= 0.0544
  HOMO = 0.0364990694340594  LUMO = 0.0474427557150424
cycle= 10 E= -1896.7152358107  delta_E= 3.67e-06  |g|= 0.0084  |ddm|= 0.0295
  HOMO = 0.0365336124903097  LUMO = 0.0474491175460584
cycle= 11 E= -1896.71524636247  delta_E= -1.06e-05  |g|= 0.00676  |ddm|= 0.00322
  HOMO = 0.0366017736594429  LUMO = 0.047448041474264
cycle= 12 E= -1896.71526775901  delta_E= -2.14e-05  |g|= 0.000148  |ddm|= 0.0123
  HOMO = 0.0366082495934922  LUMO = 0.0474502510189246
cycle= 13 E= -1896.71526773028  delta_E= 2.87e-08  |g|= 0.00029  |ddm|= 0.000738
  HOMO = 0.0366070772709539  LUMO = 0.0474497552110433
cycle= 14 E= -1896.71526773753  delta_E= -7.25e-09  |g|= 0.000254  |ddm|= 9.31e-05
  HOMO = 0.0366057471473882  LUMO = 0.047450089677829
cycle= 15 E= -1896.71526776261  delta_E= -2.51e-08  |g|= 0.000104  |ddm|= 0.000279
  HOMO = 0.0366050578034793  LUMO = 0.0474502809637383
cycle= 16 E= -1896.71526776748  delta_E= -4.87e-09  |g|= 2.15e-05  |ddm|= 0.000155
  HOMO = 0.0366049440679104  LUMO = 0.0474502141823837
cycle= 17 E= -1896.71526776757  delta_E= -8.55e-11  |g|= 1.43e-05  |ddm|= 1.47e-05
converged SCF energy = -1896.71526776757
Running TDDFT in current process (force_single_gpu=True)


******** <class 'gpu4pyscf.tdscf.rks.TDDFT'> for <class 'gpu4pyscf.dft.rks.RKS'> ********
nstates = 3 triplet
deg_eia_thresh = 1.000e-03
wfnsym = None
conv_tol = 1e-05
eigh lindep = 1e-12
eigh level_shift = 0
eigh max_cycle = 100
chkfile = molecule_alone.chk
max_memory 4000 MB (current use 1787 MB)


Excited State energies (eV)
[0.32692843 0.48082886 1.30711684]
Combined effects: {'t1_exe_effect': 0.006223348148195473, 't2_exe_effect': 0.00753857832751148, 't3_exe_effect': 0.006617431327275103}

Final statistics written to: logs_20260905_170738/calculation_summary.out
Raw properties appended to: logs_20260905_170738/calculation_summary.out
Created: ligand_t1_exe.mol2
Created: ligand_t2_exe.mol2
Created: ligand_t3_exe.mol2
Created: ligand_t1_exe_normalized.mol2
Created: ligand_t2_exe_normalized.mol2
Created: ligand_t3_exe_normalized.mol2

Created: ligand_tuning_summary.csv

Organizing results into: results_ligand_2026-09-05_17-10-14/
  Moved: ligand_tuning_summary.csv
  Moved 6 MOL2 files
  Added normalization parameters to summary
  Moved: logs_20260905_170738/ -> logs/
All expected output files were created.
